The IRS guidance is more of direction to avoid double dipping. If the property is sold, then you can take those expenses as part of the basis/expense of sale. If it is rented, you can take them off on Schedule E. But, you can't take them both places.
As far as "loss of income due to vacancy," this is simply stating if the property sits unrented for say 3 months, and you normally rent it for $1000/month, you can't take a $3000 deduction for the rent you didn't get.
